Zobrazeno 1 - 10
of 39
pro vyhledávání: '"José S, Duca"'
Publikováno v:
Journal of chemical information and modeling. 61(12)
Relative binding free-energy (RBFE) calculations are experiencing resurgence in the computer-aided drug design of novel small molecules due to performance gains allowed by cutting-edge molecular mechanic force fields and computer hardware. Applicatio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17bf389999af4b4bf8d5e4148cb84035
https://pubmed.ncbi.nlm.nih.gov/34843243
https://pubmed.ncbi.nlm.nih.gov/34843243
Autor:
C. Wartchow, José S. Duca, Vibhas Aravamuthan, Sarah Williams, Robert A. Pearlstein, Hongbin Wan
Cellular functions are executed via a form of analog computing that is based on the switchable covalent and non-covalent states of multi-molecular fluxes (i.e., time-dependent species/state concentrations) operating in the non-linear dynamics regime.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::a24c93ff0be1b86fc3ac531cae7b8e41
https://doi.org/10.1101/2021.10.29.466510
https://doi.org/10.1101/2021.10.29.466510
Autor:
Matthias Zentgraf, Elizabeth Krutoholow, Thomas S. Rush, Chris Luebkemann, Kimito Funatsu, Gisbert Schneider, Jeff Blaney, Alleyn T. Plowright, Norman Sieroka, John Edward Hill, Petra Schneider, Jennifer Listgarten, José S. Duca, Robert Alan Goodnow, Johanna M. Jansen, Jasmin Fisher, Matthias Kohler, W. Patrick Walters
Publikováno v:
Nature Reviews Drug Discovery. 19:353-364
Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by such tools, others remain sceptical, waiting for a clear impact to be shown in drug discov
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::53001ef1a373cf62d629543029f92869
https://doi.org/10.1038/s41573-019-0050-3
https://doi.org/10.1038/s41573-019-0050-3
Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability
Autor:
Anastasia Theodoropoulou, Camilo Velez-Vega, Ioannis Andreadelis, Zoe Cournia, Sofia Kiriakidi, José S. Duca, John I. Manchester, Christos Lamprakis, Stefan Doerr, Alexios Chatzigoulas
Ras proteins are membrane-anchored GTPases that regulate key cellular signaling networks. It has been recently shown that different anionic lipid types can affect the properties of Ras in terms of dimerization/clustering on the cell membrane. To unde
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::63841579a7ef7effee5d356e96d04aa8
https://doi.org/10.26434/chemrxiv-2021-4pdzb
https://doi.org/10.26434/chemrxiv-2021-4pdzb
Autor:
Christos Lamprakis, Camilo Velez-Vega, José S. Duca, Zoe Cournia, Ioannis Andreadelis, John I. Manchester
Publikováno v:
Journal of chemical theory and computation. 17(5)
Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34f804fbdda326f165ee69830e20fcf0
https://pubmed.ncbi.nlm.nih.gov/33913726
https://pubmed.ncbi.nlm.nih.gov/33913726
Autor:
Micholas Dean Smith, Jerry M. Parks, Daniel W. Kneller, Jeremy C. Smith, Andrei Golosov, Leighton Coates, Isabella Daidone, Camilo Velez-Vega, Atanu Acharya, Chris Chipot, Callum J. Dickson, Diane L. Lynch, Anna Pavlova, Yui Tik Pang, José S. Duca, James C. Gumbart, Josh V. Vermaas, Andrey Kovalevsky, Laura Zanetti-Polzi
Publikováno v:
Chemical science (Camb. 2010. Online) 12 (2021): 1513–1527. doi:10.1039/d0sc04942e
info:cnr-pdr/source/autori:Pavlova A.; Lynch D.L.; Daidone I.; Zanetti-Polzi L.; Smith M.D.; Chipot C.; Kneller D.W.; Kovalevsky A.; Coates L.; Golosov A.A.; Dickson C.J.; Velez-Vega C.; Duca J.S.; Vermaas J.V.; Pang Y.T.; Acharya A.; Parks J.M.; Smith J.C.; Gumbart J.C./titolo:Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease/doi:10.1039%2Fd0sc04942e/rivista:Chemical science (Camb. 2010. Online)/anno:2021/pagina_da:1513/pagina_a:1527/intervallo_pagine:1513–1527/volume:12
Chemical Science
bioRxiv
info:cnr-pdr/source/autori:Pavlova A.; Lynch D.L.; Daidone I.; Zanetti-Polzi L.; Smith M.D.; Chipot C.; Kneller D.W.; Kovalevsky A.; Coates L.; Golosov A.A.; Dickson C.J.; Velez-Vega C.; Duca J.S.; Vermaas J.V.; Pang Y.T.; Acharya A.; Parks J.M.; Smith J.C.; Gumbart J.C./titolo:Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease/doi:10.1039%2Fd0sc04942e/rivista:Chemical science (Camb. 2010. Online)/anno:2021/pagina_da:1513/pagina_a:1527/intervallo_pagine:1513–1527/volume:12
Chemical Science
bioRxiv
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been det
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::db05abd3afa28ed59d184b59fb815e36
https://pubs.rsc.org/en/content/articlelanding/2021/SC/D0SC04942E#!divAbstract
https://pubs.rsc.org/en/content/articlelanding/2021/SC/D0SC04942E#!divAbstract
Autor:
Subarna Shakya, José S. Duca, Elizabeth R. Sprague, Xin Chen, Zhuoliang Chen, Carol Joud, Yaping Wang, John William Giraldes, Wenlin Shao, Simon Mathieu, Chen Christine Hiu-Tung, Yanqiu Yuan, Kristen Hurov, B. Barry Touré, Christopher Sean Straub
Publikováno v:
Journal of Medicinal Chemistry. 60:2155-2161
While adding the structural features that are more favored by on-target activity is the more common strategy in selectivity optimization, the opposite strategy of subtracting the structural features that contribute more to off-target activity can als
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6bfbe2e1bd93085f79063c4dc5fd61bb
https://doi.org/10.1021/acs.jmedchem.7b00033
https://doi.org/10.1021/acs.jmedchem.7b00033
Publikováno v:
Journal of chemical information and modeling. 60(1)
The Kv11.1 potassium channel, encoded by the human ether-a-go-go-related gene (hERG), plays an essential role in the cardiac action potential. hERG blockade by small molecules can induce "torsade de pointes" arrhythmias and sudden death; as such, it
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6310085c798f25a01339e45e6258715b
https://pubmed.ncbi.nlm.nih.gov/31880933
https://pubmed.ncbi.nlm.nih.gov/31880933
Autor:
Petra, Schneider, W Patrick, Walters, Alleyn T, Plowright, Norman, Sieroka, Jennifer, Listgarten, Robert A, Goodnow, Jasmin, Fisher, Johanna M, Jansen, José S, Duca, Thomas S, Rush, Matthias, Zentgraf, John Edward, Hill, Elizabeth, Krutoholow, Matthias, Kohler, Jeff, Blaney, Kimito, Funatsu, Chris, Luebkemann, Gisbert, Schneider
Publikováno v:
Nature reviews. Drug discovery. 19(5)
Artificial intelligence (AI) tools are increasingly being applied in drug discovery. While some protagonists point to vast opportunities potentially offered by such tools, others remain sceptical, waiting for a clear impact to be shown in drug discov
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::3b4340fe33dcb827c37bc8bd01eead2f
https://pubmed.ncbi.nlm.nih.gov/31801986
https://pubmed.ncbi.nlm.nih.gov/31801986
Autor:
Tom Kurtzman, José S. Duca, Callum J. Dickson, David Ryan Koes, Steven Ramsey, Lieyang Chen, Anthony Cruz, Viktor Hornak
Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to distinguish binding from non-binding ligands for virtual screening. However, the dearth of reliab
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::798176a7370393047999e5e0b30cab0b
https://doi.org/10.26434/chemrxiv.7886165.v1
https://doi.org/10.26434/chemrxiv.7886165.v1